### Abstract

PSSMs (Position-Specific Score Matrices) have been applied to various problems in Bioinformatics. We study the following problem: given positive examples (sequences) andnegative examples (sequences), finda PSSM which correctly discriminates between positive andnegative examples. We prove that this problem is solvedin polynomial time if the size of a PSSM is bounded by a constant. On the other hand, we prove that this problem is NP-hard if the size is not bounded. We also prove similar results on deriving a mixture of PSSMs.

Original language | English |
---|---|

Title of host publication | Combinatorial Pattern Matching - 13th Annual Symposium, CPM 2002, Proceedings |

Editors | Alberto Apostolico, Masayuki Takeda |

Publisher | Springer Verlag |

Pages | 168-177 |

Number of pages | 10 |

ISBN (Electronic) | 9783540438625 |

Publication status | Published - Jan 1 2002 |

Externally published | Yes |

Event | 13th Annual Symposium on Combinatorial Pattern Matching, CPM 2002 - Fukuoka, Japan Duration: Jul 3 2002 → Jul 5 2002 |

### Publication series

Name | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
---|---|

Volume | 2373 |

ISSN (Print) | 0302-9743 |

ISSN (Electronic) | 1611-3349 |

### Other

Other | 13th Annual Symposium on Combinatorial Pattern Matching, CPM 2002 |
---|---|

Country | Japan |

City | Fukuoka |

Period | 7/3/02 → 7/5/02 |

### Fingerprint

### All Science Journal Classification (ASJC) codes

- Theoretical Computer Science
- Computer Science(all)

### Cite this

*Combinatorial Pattern Matching - 13th Annual Symposium, CPM 2002, Proceedings*(pp. 168-177). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2373). Springer Verlag.

**On the complexity of deriving position specific score matrices from examples.** / Akutsu, Tatsuya; Bannai, Hideo; Miyano, Satoru; Ott, Sascha.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

*Combinatorial Pattern Matching - 13th Annual Symposium, CPM 2002, Proceedings.*Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 2373, Springer Verlag, pp. 168-177, 13th Annual Symposium on Combinatorial Pattern Matching, CPM 2002, Fukuoka, Japan, 7/3/02.

}

TY - GEN

T1 - On the complexity of deriving position specific score matrices from examples

AU - Akutsu, Tatsuya

AU - Bannai, Hideo

AU - Miyano, Satoru

AU - Ott, Sascha

PY - 2002/1/1

Y1 - 2002/1/1

N2 - PSSMs (Position-Specific Score Matrices) have been applied to various problems in Bioinformatics. We study the following problem: given positive examples (sequences) andnegative examples (sequences), finda PSSM which correctly discriminates between positive andnegative examples. We prove that this problem is solvedin polynomial time if the size of a PSSM is bounded by a constant. On the other hand, we prove that this problem is NP-hard if the size is not bounded. We also prove similar results on deriving a mixture of PSSMs.

AB - PSSMs (Position-Specific Score Matrices) have been applied to various problems in Bioinformatics. We study the following problem: given positive examples (sequences) andnegative examples (sequences), finda PSSM which correctly discriminates between positive andnegative examples. We prove that this problem is solvedin polynomial time if the size of a PSSM is bounded by a constant. On the other hand, we prove that this problem is NP-hard if the size is not bounded. We also prove similar results on deriving a mixture of PSSMs.

UR - http://www.scopus.com/inward/record.url?scp=35248879785&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=35248879785&partnerID=8YFLogxK

M3 - Conference contribution

AN - SCOPUS:35248879785

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 168

EP - 177

BT - Combinatorial Pattern Matching - 13th Annual Symposium, CPM 2002, Proceedings

A2 - Apostolico, Alberto

A2 - Takeda, Masayuki

PB - Springer Verlag

ER -